Commit c780b8ee authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Add all metAMOS scripts

parent 6154fc84
The sample names used in the paper are named differently within the file
system:
1. The simulated mock (SM) community dataset is named either "simDat" or "simulated_data".
2. The human fecal (HF) community dataset is named X310763260.
3. The wastewater (WW) sludge community dataset is named A02.
1. The simulated mock (SM) community dataset
2. The human fecal (HF1-5) community datasets
3. The wastewater (WW1-4) sludge community datasets
4. The production scale anaerobic biogas (BG) reactor dataset
There are a total of six launcher scripts. Precisely, two (2) launcher scripts for each sample:
Two (2) commands are launched for each dataset
1. Running metAmos on default mode (SOAPdenovo assembler)
2. Running metAmos on using IDBA-UD assembler
1. Running metAMOS with only the MG data
2. Running metAMOS with both MG and MT data
3. Running metAMOS with both MT data
For the IDBA-UD based assemblies, libraries require concatenation prior to
using them as input for the pipeline (commands within script).
#!/bin/bash -l
### This script runs metAmos, using IDBA-UD as the assembler, on the simulated mock (SM) dataset
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
## Concatenate the fastq files
# For some reason, metAmos on IDBA-UD does parse the second library into the assembly step (with IDBA-UD).
# Therefore, the files are first concatenated prior to running metAmos
cat \
/mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq \
/mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq > \
/mnt/md1200/snarayanasamy/IMP_data/A02/A02_MGMT.R1.fq
cat \
/mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq \
/mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq > \
/mnt/md1200/snarayanasamy/IMP_data/A02/A02_MGMT.R2.fq
## Run metAmos with IDBA_UD
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/A02/A02_MGMT.R1.fq \
-2 /mnt/md1200/snarayanasamy/IMP_data/A02/A02_MGMT.R2.fq \
......
#!/bin/bash -l
### This script runs metAmos (default) on the simulated mock (SM) dataset
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
## Run metAmos
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MGMT/A02_metAmos_MGMT"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq,/mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq -2 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq,/mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq -d ./A02_metAmos -i 250:500,250:500
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq,/mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq -2 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq,/mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq -d $OUTDIR -i 250:500,250:500
runPipeline -d ./A02_metAmos -p 8
runPipeline -d $OUTDIR -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/A02_metAmos_MG-IDBAUD"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq -2 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8 -a idba-ud
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/A02_metAmos_MG"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R1_001.fastq -2 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux_Lipids_Community-250111_DNA_TACTTCGG_L007_R2_001.fastq -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MT_only/A02_metAmos_MT-IDBAUD"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq -2 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8 -a idba-ud
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MT_only/A02_metAmos_MT"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R1_001.fastq -2 /mnt/md1200/snarayanasamy/IMP_data/A02/Lux-Lipids-Community-RNAlater-50ng_CGATGT_L006_R2_001.fastq -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MGMT/D32_metAmos_MGMT-IDBAUD"
date
bzcat /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R1_001.fastq.bz2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R1_001.fastq.bz2 > /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT-D32_R1.fastq
bzcat /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R2_001.fastq.bz2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R2_001.fastq.bz2 > /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT-D32_R2.fastq
initPipeline -1 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT-D32_R1.fastq -2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT-D32_R2.fastq -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 16 -a idba-ud
#rm -rf /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT-D32_R1.fastq
#rm -rf /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT-D32_R2.fastq
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
date
initPipeline -1 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R1_001.fastq.bz2,/mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R2_001.fastq.bz2,/mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R2_001.fastq.bz2 -d ./D32_metAmos_MGMT -i 250:500,250:500
runPipeline -d ./D32_metAmos_MGMT -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/D32_metAmos_MG-IDBAUD"
date
initPipeline -1 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 16 -a idba-ud
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/D32_metAmos_MG"
date
initPipeline -1 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D32/LAO_Metagenome-D32_TACCGAGC_L004_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MT_only/D32_metAmos_MT-IDBAUD"
date
initPipeline -1 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8 -a idba_ud
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MT_only/D32_metAmos_MT"
date
initPipeline -1 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D32/LAO_Metatranscriptome-D32_TAGCTT_L003_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/D36/D36_MGMT.R1.fq \
-2 /mnt/md1200/snarayanasamy/IMP_data/D36/D36_MGMT.R2.fq \
-d /home/snarayanasamy/Work/metAmosAnalysis/D36_metAmos-IDBAUD_corrected -i 250:500,250:500
runPipeline -d /home/snarayanasamy/Work/metAmosAnalysis/D36_metAmos-IDBAUD_corrected -p 16 -a idba-ud
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R1_001.fastq.bz2,/mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R2_001.fastq.bz2,/mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R2_001.fastq.bz2 -d /home/snarayanasamy/Work/metAmosAnalysis/D36_metAmos -i 250:500,250:500
runPipeline -d /home/snarayanasamy/Work/metAmosAnalysis/D36_metAmos -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/D36_metAmos_MG-IDBAUD"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8 -a idba-ud
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/D36_metAmos_MG"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metagenome_D36_TTACTCGC_L007_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MT_only/D36_metAmos_MT-IDBAUD"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 16 -a idba-ud
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MT_only/D36_metAmos_MT"
date
initPipeline -1 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R1_001.fastq.bz2 -2 /mnt/md1200/snarayanasamy/IMP_data/D36/LAO_Metatranscriptome_D36_CGATGT_L006_R2_001.fastq.bz2 -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 8
date
#!/bin/bash -l
export PATH=$PATH:/home/snarayanasamy/Work/tools/metAMOS-1.5rc3/
OUTDIR="/mnt/md1200/snarayanasamy/metAmosAnalysis/LAO_MGMT/D49_metAmos_MGMT-IDBAUD"
date
bzcat /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D49/LAO_Metagenome_D49_TAGACGGA_L008_R1_001.fastq.bz2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D49/LAO_Metatranscriptome_D49_ATCACG_L008_R1_001.fastq.bz2 > /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT_D49_R1.fastq
bzcat /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metagenomic/time_series/D49/LAO_Metagenome_D49_TAGACGGA_L008_R2_001.fastq.bz2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/Metatranscriptomic/time_series/D49/LAO_Metatranscriptome_D49_ATCACG_L008_R2_001.fastq.bz2 > /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT_D49_R2.fastq
initPipeline -1 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT_D49_R1.fastq -2 /mnt/md1200/snarayanasamy/archived_raw_data/LAO/LAO_MGMT_D49_R2.fastq -d $OUTDIR -i 250:500,250:500
runPipeline -d $OUTDIR -p 16 -a idba-ud
date
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